


Consequences

by Tarlan



Category: Stargate Atlantis
Genre: Action, Angst, Comfort/Angst, Established Relationship, M/M, Post-Series, SGA Secret Santa 2014
Language: English
Status: Completed
Published: 2015-01-01
Updated: 2015-01-01
Packaged: 2018-03-04 18:11:17
Rating: Teen And Up Audiences
Warnings: Major Character Death
Chapters: 1
Words: 3,175
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/3079403
Author URL: https://archiveofourown.org/users/Tarlan/pseuds/Tarlan
Summary: <blockquote class="userstuff">
              <p>When the Daedalus arrives with shields failing and the Wraith attacking, John and Rodney know that decisions must be made quickly if they are to save the stricken ship and her crew. Some decisions have tragic consequences.<br/>Major character death not Rodney or John.</p>
            </blockquote>





	Consequences

**Author's Note:**

  * For [Gryph](https://archiveofourown.org/users/Gryph/gifts).



> Written for gryphon2k, for SGA Secret Santa 2014.  
> Gryphon2k asked for: _Rodney being Rodney. John/Rodney. But mostly I like Rodney being his annoying, arrogant, brilliant, adorable self. I like stories that tend to the angsty side of the spectrum (physical or psychological torture, character death, end of the world, it's all good). I like conflicted emotions, relationships going through turmoil. My biggest preferences is whatever is done be as cannon compliant as possible._

"If your intention was to destroy the space-time continuum then well done."

Rodney's acerbic tones echoed through the laboratory making everyone around him cringe and focus harder on their own work. John suspected that most were hoping that if they kept their heads down then they were less likely to incur the Wrath of McKay. He grimaced as the hapless Doctor Fransom took the brunt of Rodney's irritation on this occasion, but under the circumstances perhaps Fransom deserved it. No one should be messing with the Space-Time continuum; though he wasn't going to mention the exception where one version of Rodney spent twenty-five years working out a way to bring him home after a Stargate malfunction sent him 48 thousand years into the future, destroying that original timeline in the process.

Before Rodney could continue with his tirade, the strident Ancient alarm sounded throughout the city. John's eyes met Rodney's startled blue before they moved as one, racing from the laboratory towards the transporter. Within a minute they were entering the control room above the Stargate, and John watched as Rodney shoved the sergeant monitoring the sensors aside, swiftly taking control. The sergeant merely rolled his eyes and started operating another console.

"It's the _Daedalus_ ," Rodney exclaimed before looking over his shoulder at John. "And she's coming in hot."

A projection appeared above the monitor and John could see the larger shape of the _Daedalus_ being pursued by a Hive ship and dozens of smaller craft - Wraith darts. John turned to Woolsey, who seemed to know exactly what John was going to say because he nodded towards the Jumper Bay.

"Go," Woolsey ordered, and John was on his radio immediately, ordering pilots to their Jumpers.

He left his mike open on the command channel, listening in as Rodney began listing the damage to the _Daedalus_.

"Hyperdrive drive is down. Weapons are offline. Numerous casualties reported. Shields are fail... Shields have failed." A pause. "Transporter is offline," he added softly.

John could imagine Rodney looking up at Woolsey in desperation, aware that the _Daedalus_ was a sitting duck without weapons and a means to safely evacuate its 250 crew using the Asgard beaming technology. The distressed ship and her crew had only one hope of salvation and that was reaching Atlantis and the protection of her stronger shields.

By now John was already inside his puddlejumper and rising towards the roof access with Lorne and several others following. As he rose above the city he heard Rodney continue, his tone sharp.

"If we don't lower the shield and let them land-."

"Lower the shield," Woolsey ordered. It was a calculated risk with so many Wraith darts already hounding the damaged ship but John was glad Woolsey made the call.

Carson chimed in. "Medical personnel are heading to the east pier ready to transport injured crew to the Infirmary."

As the shield lowered, John headed straight for the _Daedalus_ , sending drones after the darts closest to the stricken ship before they could engage their culling beams. Their attempts to outmaneuver the drones failed, with the darts turning into fireballs that rained down on the city below. He pulled up hard, skimming the side of the _Daedalus_ as it continued on down, picking off another dart that was too close for comfort and seeing other darts explode as Lorne and the other pilots engaged the Wraith. John cursed when several darts broke away from the main force, taking advantage of the lowered shield to attack the city.

"Lorne-."

"On it."

Lorne and one other jumper veered off to chase down the darts while John followed the _Daedalus_ down to the east pier, protecting her as best he could. He frowned as a dart screamed by him.

"McKay! The shield!" he yelled when he realized it was still down, allowing more darts to attack the city directly.

"I'm trying!"

By now the _Daedalus_ was landing and John frowned when he saw one of the medical teams racing across the pier towards it.

"Beckett, tell your teams to stay back until-."

He never finished the sentence, watching in dismay as a dart skimmed the pier, scooping up most of the medical team in its culling beam. John gave chase as the shield began to rise around the city. Banking at the last moment, he barely avoided being hit with debris as the dart impacted against the inside of the shield. Quickly he compartmentalized the loss of the culled personnel as he joined Lorne and the others in bringing down the remaining trapped darts, determined that no more of his people would be taken this day. Once the last dart was destroyed, John ordered all the jumpers back to the Jumper bay.

When he reached the control room minutes after landing, it was a hive of activity with every console manned and operational. John spotted Fransom working on the internal sensors, sweeping the city, but he turned his attention to Rodney. Rodney looked pale with shock, his voice holding a slight tremor as he gave orders to his teams of scientists.

"Rodney?"

Pausing, Rodney turned to him and stared for just a split second, his voice breaking as he said a single word, "Jennifer..."

John swallowed hard, not needing to hear the rest. He'd seen the group of medics taken by the culling beam, and he'd seen that same dart explode against the shield. Jennifer must have been among them. Reaching out, he rested his hand on Rodney's shoulder and squeezed gently, feeling the tremors racing through Rodney's body. He wished he had time to offer more than this small gesture of comfort but they had more pressing issues right now, including the possibility of Wraith in the city.

"Status update? Rodney," he shook him slightly and repeated, "Status update."

Rodney stood up taller and reported back. "The Hive ship took extensive damage and is retreating. Sensors show no Wraith beamed into the city... and no one else has been reported missing."

One advantage of having been on Earth for several months was the chance to upgrade the internal sensors to cover the whole city. Even a hibernating Wraith would register now, so the chances of another Bob sneaking around Atlantis were slim to nonexistent. The new sensors were sensitive enough to register any Wraith transmitters too, though John wanted manual checks of all areas touched by a culling beam nonetheless. Woolsey moved over to join him and Rodney.

"We need to move the city," John stated softly, aware that their current location had been compromised. If the Hive joined forces with another Queen then they could easily face another siege like the one in their first year on Atlantis.

Woolsey nodded in agreement. "Doctor McKay?" he asked.

"Yes. Yes. The secondary landing site should-."

A call from Radek caught their attention. "My team has found dart debris from the one that swept up our people. The transformer and storage unit are damaged but I think I can make repairs."

His words snapped Rodney out of his shock, eyelids blinking rapidly as his big brain churned over the new information, hope blossoming in his eyes. "We may be able to save our people." He glanced around, frowning and snapping his fingers. "You! Frankincense. What are you waiting for? A personal invitation?"

Fransom startled but quickly grabbed whatever equipment he needed before running after Rodney, who was already halfway to the transporter by then. John caught up with Rodney first, grabbing his arm.

"McKay! We need to move the city... NOW."

"Yes. Yes, of course." He turned to the scientist who had stopped beside them. "Handsome?"

Fransom smirked but didn't correct Rodney. "I'll get to work on the pattern matrix with Doctor Zelenka." He moved off quickly.

"You know his name is Fransom," John stated softly, though it was an amusing mistake.

"Huh?"

"Never mind," John shook his head, deciding he needed Rodney to focus on the city rather than on anything else right now.

Together they headed towards the Chair Room and within half an hour John's thoughts were deeply meshed with Atlantis, igniting the star drive and guiding the city as she rose from the sea and took flight.

Before they left Earth several months earlier, they had chosen five potential landing sites within Pegasus just in case the primary or secondary sites were compromised in any way. The second choice was the world where the Atlantis Expedition had originally found the lost city beneath the waves and later abandoned following the Asuran attack - Lantea. The ocean covered most of the surface so Rodney and his team had picked out an area thousands of miles away from the original resting place, just to be on the safe side.

John settled into the Chair for the three hour flight, glad Atlantis was able to compensate for his occasional wandering thoughts. If anything he felt as if Atlantis was trying to comfort him as he dwelt on memories of Rodney and Jennifer Keller, and on him and Rodney. 

It was only a few months earlier that Rodney and Jennifer had decided that their relationship wasn't going anywhere, agreeing to remain friends, and surprisingly they had made it work. It hadn't stopped John from experiencing small pangs of jealousy whenever he saw them eating lunch together or meeting for a coffee in the mess, but he could never begrudge Rodney having another close friend. Rodney and Jennifer were rarely alone together for long anyway, with others joining them regularly.

John was the only one who never went over unless the rest of the team or Carson or Radek was already there. It wasn't because he disliked Jennifer; he simply felt awkward around her when it was just Rodney present, as if he was intruding on their friendship. Except that wasn't strictly true, but he wasn't going to admit out loud how much it still bothered him to see Rodney with Jennifer. She was smart and pretty, and although he had never been too keen on her methods, he had applauded her continued efforts to make Rodney pay more attention to the feelings of others.

The simple truth was that he had hated watching Rodney find love with someone - hell, with anyone else. It was immature and selfish, and in some ways John had been glad Jennifer's lessons on empathy hadn't taken root because at least Rodney had remained oblivious to John's desire for him - until John made one slip too many.

He smiled wryly at the memory of snapping fingers and accusations from a too sharp mind; of the fear of discovery ending in a bone-melting kiss.

This change in his relationship with Rodney was still so new, so fragile. He was still convinced it was either a really good dream or simply too good to be true. The last few nights had been... amazing. He could still feel the soft, slickness of Rodney's skin sliding against his own, and feel the power of strong muscles pressing him down, holding him tight as they moved together. He'd always wondered if Rodney would be as good at kissing as he was at talking... and now he knew he was even better, recalling how Rodney had slowly taken him apart last night, driving him almost insane with desire before finally allowing him to come.

Amazing, beautiful... bossy. He smiled wider, remembering how it felt to wake up with Rodney lying beside him this morning, naked and warm, and demanding coffee. He wanted that every day for the rest of his life.

A mental alert pulled his attention back to the city.

"Problem with the weight distribution?" Rodney asked. 

"Correcting it now." John gave a small nudge that leveled off the city in flight, keeping her on course for Lantea.

Hours later, John closed his eyes to shut out all external stimuli as he carefully settled Atlantis back onto the Lantean Ocean, making only the smallest of waves despite the size of the city and the additional weight she carried in the form of the _Daedalus_. He opened his eyes to find Caldwell propped up against the wall by the door, looking like he might fall over with just a gentle nudge. The stark white of a crisp bandage wrapped around his head almost blended into the paleness of his face and John wondered if Caldwell was supposed to be out of the infirmary.

John flicked his eyes across to where Rodney was still going through streams of data, smirking when it became obvious that Rodney had not noticed Caldwell's presence.

"Considering the dead weight on the east pier, that wasn't a bad lan... Colonel Caldwell."

"Doctor McKay," Caldwell responded coolly, though the twitch of his lips proved he was not too annoyed at McKay for calling his ship a dead weight. It was the truth after all.

"Um. We'll start on repairs as soon as humanly possible."

This time Caldwell did smile just a fraction more. "I'm not here to harangue you, Doctor McKay. I'm here to thank you on behalf of my crew."

"Oh. Well. Obviously." Rodney looked to John for guidance, looking confused.

"We'll pass the thanks along to Doctor Z and the others," John responded far more diplomatically.

Before it could get any more uncomfortable, a call came in from Radek.

"We are ready to retrieve our personnel from the Dart."

"On our way," John stated.

Ten minutes later, with the Wraith device hooked up to an external power source, everyone tensed as Radek brought up the pattern matrix.

"What is it?" John asked.

"Five of our people are missing and a further four from the _Daedalus_ , though there is no guarantee that this was the same dart that scooped them all up. However, the pattern buffer reads ten retrievable individuals." Radek blinked over the top of his glasses. "There were at least seventeen other patterns present but they have degraded too far from damage to the unit."

"Some of these, or all of them, could be Wraith," Ronon stated, drawing his blaster and setting it on kill.

John nodded in agreement, having seen the Wraith use the beam to drop Boneheads on the ground during a culling. He tapped his radio. "Security to Lab 4-Alpha." He looked around. "I want all non-essential personnel to leave now, and I want the lab sealed. Full containment protocols."

Once the security detail was in position around the laboratory, Rodney activated the process to reverse the culling beam, and John saw Rodney's chin rise defiantly as the figures appeared; three of them were Wraith. The seven humans froze momentarily before falling to the ground, stunned, which suited John just fine. Shots rang out before the Wraith had a chance to raise their stunners, all of them falling under a hail of bullets, and blasts from Ronon's hand gun.

When the last of the Wraith was dead, John and Ronon checked the human survivors; three of them wore the uniform of _Daedalus_ crew members, and although the remainder were from the medical unit, Jennifer Keller was not among them.

John saw the grief and self-recrimination already forming on Rodney shocked face as wide blue eyes passed over the bloody scene and the unconscious survivors before landing on John.

He knew Rodney had been so pleased with himself for persuading Jennifer to return to Pegasus - even though Carson had already accepted the post of Chief Medical Officer. Added to this, Rodney had been the one to lower the shield when the _Daedalus_ came limping into orbit with Wraith darts hounding it and he was the one unable to raise it fast enough once the _Daedalus_ was inside the shield's protective radius, so of course Rodney would blame himself for her loss.

Except it wasn't his fault, or Caldwell's. The Wraith were to blame.

Leaving Ronon in charge of clearing away the Wraith bodies and Carson in taking the surviving humans down to the infirmary to be checked over, John caught Rodney's arm and steered him from the laboratory. When John had almost reached his quarters Rodney stopped and turned to him, all the horror and distress reflected in his wide blue eyes.

"This is all my fault," he whispered hoarsely.

John felt his heart break a little as he grabbed Rodney by his biceps. "No. It wasn't."

A couple of scientists entered the corridor further back so John pulled him along the final few feet and into his quarters. He pressed Rodney's shoulder to make him sit on the edge of the bed where they had awoken in each other's arms only this morning. That was only a little over fourteen hours ago and yet it felt as if a lifetime had passed since then. Technically they were both off duty now but John quickly updated Woolsey anyway before moving round the room to where he kept his personal stash. He poured two glasses of whiskey and handed one to Rodney.

Rodney stared down into the amber liquid without really seeing it.

"Jennifer... Jennifer didn't want to come back. She... I forced her-."

"No." John barked out sharply, startling Rodney enough to raise his head. "You didn't force her to do anything. You never could."

Jennifer was tougher than most believed; pre-judging her by her age. She could be as stubborn and tenacious as Rodney, and he knew for a fact that the reason why she had chosen to come back was mostly because Carson had taken over the CMO position, leaving her more time for her own research. She'd never particularly liked all the paperwork and management that came with the CMO position, having never quite learned the art of delegation.

John crouched down in front of Rodney, resting his hands on Rodney's knees.

"It wasn't your fault," he continued softly. "You reminded her of all the good that was here. All the discoveries to be made. She knew the risks and she wanted to be here, Rodney, just as much as you."

Rodney shot back the whiskey, grimacing and coughing slightly before setting aside the tumbler. He leaned forward until their foreheads were touching, and John closed his eyes, breathing in the presence of this precious man. Eventually they moved, heads tilting until John could feel the press of Rodney's lips against his, bittersweet with loss.

Rodney pulled back a fraction. "Can I... stay tonight?"

John reached up to cup his face in both hands. "Every night," he answered softly.

Later, as he held Rodney close, he thought about Jennifer and all the missed opportunities to get to know her due to his own insecurities. He thought of all the lost time too, while hiding his feelings for Rodney; time that they could have spent wrapped in each other's arms, loved and beloved.

No more wasted time though. Tomorrow he would ask Rodney to move into shared quarters with him, and even though this part of their relationship was shiny and new, he never doubted for a moment that Rodney would say yes. They belonged together, for as long as the universe would allow.

END  
.


End file.
